Climate change has the potential to alter the flow regimes of rivers and consequently affect the taxonomic and functional diversity of freshwater organisms. We modeled future flow regimes for the 2050 and 2090 time horizons and tested how flow regimes impact the abundance of 150 macroinvertebrate species and their functional trait compositions in one lowland river catchment (Treene) and one mountainous river catchment (Kinzig) in Europe. We used all 16 global circulation models (GCMs) and regional climate models (RCMs) of the CORDEX dataset under the RCP 8.5 scenario to calculate future river flows. The high variability in relative change of flow among the 16 climate models cascaded into the ecological models and resulted in substantially different predicted abundance values for single species. This variability also cascades into any subsequent analysis of taxonomic or functional freshwater biodiversity. Our results showed that flow alteration effects are different depending on the catchment and the underlying species pool. Documenting such uncertainties provides a basis for the further assessment of potential climate-change impacts on freshwater taxa distributions.